Design and synthesis of non-peptide mimetics mapping the immunodominant myelin basic protein (MBP83–96) Epitope to function as T-cell receptor antagonists

Encephalitogenic T cells are heavily implicated in the pathogenesis of multiple sclerosis (MS), an autoimmune demyelinating disease of the central nervous system. Their stimulation is triggered by the formation of a trimolecular complex between the human leukocyte antigen (HLA), an immunodominant myelin basic protein (MBP) epitope, and the T cell receptor (TCR). We detail herein our studies directed towards the rational design and synthesis of non-peptide mimetic molecules, based on the immunodominant MBP83–96 epitope that is recognized by the TCR in complex with HLA. We focused our attention on the inhibition of the trimolecular complex formation and consequently the inhibition of proliferation of activated T cells. A structure-based pharmacophore model was generated, in view of the interactions between the TCR and the HLA-MBP83–96 complex. As a result, new candidate molecules were designed based on lead compounds obtained through the ZINC database. Moreover, semi-empirical and density functional theory methods were applied for the prediction of the binding energy between the proposed non-peptide mimetics and the TCR. We synthesized six molecules that were further evaluated in vitro as TCR antagonists. Analogues 15 and 16 were able to inhibit to some extent the stimulation of T cells by the immunodominant MBP83–99 peptide from immunized mice. Inhibition was followed to a lesser degree by analogues 17 and 18 and then by analogue 19. These studies show that lead compounds 15 and 16 may be used for immunotherapy against MS

Space-partitioning with cascade-connected ANN structures for positioning in mobile communication systems

The world around us is getting more connected with each day passing by – new portable devices employing wireless connections to various networks wherever one might be. Locationaware computing has become an important bit of telecommunication services and industry. For this reason, the research efforts on new and improved localisation algorithms are constantly being performed. Thus far, the satellite positioning systems have achieved highest popularity and penetration regarding the global position estimation. In spite the numerous investigations aimed at enabling these systems to equally procure the position in both indoor and outdoor environments, this is still a task to be completed. This research work presented herein aimed at improving the state-of-the-art positioning techniques through the use of two highly popular mobile communication systems: WLAN and public land mobile networks. These systems already have widely deployed network structures (coverage) and a vast number of (inexpensive) mobile clients, so using them for additional, positioning purposes is rational and logical. First, the positioning in WLAN systems was analysed and elaborated. The indoor test-bed, used for verifying the models’ performances, covered almost 10,000m2 area. It has been chosen carefully so that the positioning could be thoroughly explored. The measurement campaigns performed therein covered the whole of test-bed environment and gave insight into location dependent parameters available in WLAN networks. Further analysis of the data lead to developing of positioning models based on ANNs. The best single ANN model obtained 9.26m average distance error and 7.75m median distance error. The novel positioning model structure, consisting of cascade-connected ANNs, improved those results to 8.14m and 4.57m, respectively. To adequately compare the proposed techniques with other, well-known research techniques, the environment positioning error parameter was introduced. This parameter enables to take the size of the test environment into account when comparing the accuracy of the indoor positioning techniques. Concerning the PLMN positioning, in-depth analysis of available system parameters and signalling protocols produced a positioning algorithm, capable of fusing the system received signal strength parameters received from multiple systems and multiple operators. Knowing that most of the areas are covered by signals from more than one network operator and even more than one system from one operator, it becomes easy to note the great practical value of this novel algorithm. On the other hand, an extensive drive-test measurement campaign, covering more than 600km in the central areas of Belgrade, was performed. Using this algorithm and applying the single ANN models to the recorded measurements, a 59m average distance error and 50m median distance error were obtained. Moreover, the positioning in indoor environment was verified and the degradation of performances, due to the crossenvironment model use, was reported: 105m average distance error and 101m median distance error. When applying the new, cascade-connected ANN structure model, distance errors were reduced to 26m and 2m, for the average and median distance errors, respectively. The obtained positioning accuracy was shown to be good enough for the implementation of a broad scope of location based services by using the existing and deployed, commonly available, infrastructure

INFLUENCE OF FLIGHT CONFIGURATION USED FOR LiDAR DATA COLLECTION ON INDIVIDUAL TREES DATA EXTRACTION IN FOREST PLANTATIONS

AbstractIn the last decades, several studies have been conducted aiming to the extraction of forest variables from LiDAR data. Although such studies have indicated great potential, the high cost associated with LiDAR data acquisition process inhibits the technology to become an operational technique for forestry applications. The cost of a LiDAR survey, as for any other data collection techniques, is composed of fixed and variable costs. The variable portion, which can be optimized, is dependent, among other factors, on the number of flight hours. The flight time is mainly dependent on the flight configuration used for the survey. The objective of this paper is to investigate the impact of using different operational parameters on different species of forest plantations, to provide inputs for an adequate cost-benefit analysis. The different configurations are evaluated in terms of the number of individual trees automatically detected, individual height and volume, using the forest inventory as the reference data. The experiments have shown that compatible results are obtained using different configurations with flight time varying by a factor of 3.5 to 10 times. Also, for a given point density, preference should be given to the configuration based on a lower flying height.Keywords: Airborne LiDAR; remote sensing; progressive densification; forest mensuration; operational parameters; tree height; volume. ResumoInfluência da configuração de voo para aquisição de dados LiDAR na extração de dados de árvores individuais em plantios florestais. Nas últimas décadas, vários estudos têm sido realizados visando à utilização dos dados obtidos através da tecnologia LiDAR (Light Detection And Ranging) na obtenção de variáveis florestais. Embora tais estudos indiquem alto potencial do LiDAR para aplicações florestais, o elevado custo do levantamento dificulta sua operacionalização no meio florestal. O custo de um levantamento LiDAR, como em outros tipos de levantamentos, é composto de custos fixos e variáveis. A parcela de custos variáveis, a qual pode ser otimizada, encontra-se associada, dentre outros fatores, ao número de horas de voo. O tempo de voo depende principalmente da configuração de voo utilizada no levantamento. Este artigo visa analisar a influência da utilização de diferentes parâmetros operacionais para diferentes espécies de plantios florestais, objetivando prover insumos para uma adequada análise custo-benefício. As configurações são avaliadas em termos do número de árvores automaticamente identificadas, altura individual e volume, tendo como referência os dados do inventário florestal. Os experimentos realizados demonstraram que resultados comparáveis são obtidos com a utilização de diferentes configurações com tempo de voo variando de um fator de 3,5 a 10 vezes. Observou-se também que para uma dada densidade de pontos deve-se dar preferência à configuração que utilize menor altura de voo.Palavras-chave:      Laser scanner; sensoriamento remoto; parâmetros operacionais; altura; volume.In the last decades, several studies have been conducted aiming to the extraction of forest variables from LiDAR data. Although such studies have indicated great potential, the high cost associated with LiDAR data acquisition process inhibits the technology to become an operational technique for forestry applications. The cost of a LiDAR survey, as for any other data collection techniques, is composed of fixed and variable costs. The variable portion, which can be optimized, is dependent, among other factors, on the number of flight hours. The flight time is mainly dependent on the flight configuration used for the survey. The objective of this paper is to investigate the impact of using different operational parameters on different species of forest plantations, to provide inputs for an adequate cost-benefit analysis. The different configurations are evaluated in terms of the number of individual trees automatically detected, individual height and volume, using the forest inventory as the reference data. The experiments have shown that compatible results are obtained using different configurations with flight time varying by a factor of 3.5 to 10 times. Also, for a given point density, preference should be given to the configuration based on a lower flying height.Keywords: Airborne LiDAR; remote sensing; progressive densification; forest mensuration; operational parameters; tree height; volume

Estimation of forest variables using airborne laser scanning

Airborne laser scanning can provide three-dimensional measurements of the forest canopy with high efficiency and precision. There are presently a large number of airborne laser scanning instruments in operation. The aims of the studies reported in this thesis were, to develop and validate methods for estimation of forest variables using laser data, and to investigate the influence of laser system parameters on the estimates. All studies were carried out in hemi-boreal forest at a test area in southwestern Sweden (lat. 58°30’N, long. 13°40’ E). Forest variables were estimated using regression models. On plot level, the Root Mean Square Error (RMSE) for mean tree height estimations ranged between 6% and 11% of the average value for different datasets and methods. The RMSE for stem volume estimations ranged between 19% and 26% of the average value for different datasets and methods. On stand level (area 0.64 ha), the RMSE was 3% and 11% of the average value for mean tree height and stem volume estimations, respectively. A simulation model was used to investigate the effect of different scanning angles on laser measurement of tree height and canopy closure. The effect of different scanning angles was different within different simulated forest types, e.g., different tree species. High resolution laser data were used for detection of individual trees. In total, 71% of the field measurements were detected representing 91% of the total stem volume. Height and crown diameter of the detected trees could be estimated with a RMSE of 0.63 m and 0.61 m, respectively. The magnitude of the height estimation errors was similar to what is usually achieved using field inventory. Using different laser footprint diameters (0.26 to 3.68 m) gave similar estimation accuracies. The tree species Norway spruce (Picea abies L. Karst.) and Scots pine (Pinus sylvestris L.) were discriminated at individual tree level with an accuracy of 95%. The results in this thesis show that airborne laser scanners are useful as forest inventory tools. Forest variables can be estimated on tree level, plot level and stand level with similar accuracies as traditional field inventories

Mechanische Kreislaufunterstützung bei Patienten im akuten kardiogenen Shock

Objectives Cardiogenic shock (CS) as the final stage of Heart failure (HF) is present in approximately 25% of cases and is associated with high mortality. Temporary mechanical circulatory support (MCS) is widely used for CS therapy. In our research, we investigated and compared different temporary MCS concepts based on microaxial intraaortic impeller pumps. Methods The data of all patients who received MCS with a temporary microaxial left ventricular impeller pump in the German Heart Center Berlin (DHZB) since 01/2016 were collected retrospectively and used for a database establishment. The obtained data were analyzed in regard to different clinical aspects and published. This dissertation summarizes and describes the results of three major publications. Results The results of the pilot study demonstrated a 43% survival in 28 patients on isolated impeller pump support, as well as 44% in 9 CS patients on combination of v a ECLS and Impella. Preoperative cardiopulmonary resuscitation (CPR) and an arterial pH 7.45 were associated with poor outcomes. In the second study, 70 patients were supported with Impella 5.0/5.5®. The overall 30 day survival was 51%. An increase in arterial lactate (OR 1.217 per 1 mmol/L; p=0.015) and CPR before implantation (OR 16.74; p=0.009) were identified as predictors of 30 day mortality on Impella support. A cut-off of 8 mmol/L for preoperative lactate showed a specificity of 0.944 and a sensitivity of 0.294 (OR 7.083, CI 1.422 35.28; p=0.017) for 30 day mortality. Based on these data, an algorithm for optimal short-term MCS therapy was developed and thereafter applied as a standardized operational procedure at the DHZB. In my third analysis we compared the percutaneously implanted Impella CP® and larger surgical Impella 5.0/5.5®. In unadjusted cohorts the 30 day survival was significantly higher in the Impella 5.0/5.5® group (58% vs. 36%, p=0.021). After propensity score adjustment for relevant preoperative demographic and hemodynamic parameters, the 30 day survival was similar between the groups (OR 1.23, 95% CI [0.34-4.18], p=0.744). Preoperative lactate levels above 8 mmol/L and CPR before implantation were associated with poor outcomes in both cohorts (OR 10.7, 95% CI [3.45-47.34], p<0.001; OR 13.2, 95% CI [4.28-57.89], p<0.001). Based on these results the selection algorithm from the second study was amended to include the use of percutaneous impeller pumps. Conclusions A total of 203 patients treated with different MCS devices were analyzed. Our studies demonstrated that temporary MCS with microaxial impeller pumps is a feasible treatment in CS patients. In cases with preoperative CPR or lactate levels ≥ 8 mmol/L an advanced treatment concept with a combination of Impella and v a ECLS should be pursued. An algorithm based on these parameters may prove useful for optimal patient selection and to identify optimal temporary MCS in CS patients.Ziele Kardiogener Schock (KS) als Endstadium der Herzinsuffizienz (HI) tritt in ungefähr 25% der Fälle auf und ist mit einer hohen Sterblichkeit assoziiert. Temporäre mechanische Kreislaufunterstützung (MKU) wird in der Therapie des KS eigesetzt. In unseren Studien wurden verschiedene Konzepte für temporäre MKU auf der Basis der mikroaxialen int-raaortalen Impellerpumpe untersucht und verglichen. Methoden Die Daten von allen im Deutschen Herzzentrum Berlin (DHZB) seit 01/2016 zur mecha-nischen Kreislaufunterstützung mit einem temporären linksventrikulären mikroaxialen Impellersystem versorgten Patienten*innen wurden retrospektiv in einer Datenbank ge-sammelt, analysiert und publiziert. Diese Dissertation ist eine Zusammenfassung der Ergebnisse der drei wichtigsten Pub-likationen. Ergebnisse Die Ergebnisse der Pilotstudie zeigten ein Überleben von 43% bei 28 Patienten*innen unter isolierter mikroaxialer Impellerpumpentherapie, sowie 44% bei 9 Patienten*innen mit Kombination von v-a ECLS und Impella. Präoperative kardiopulmonale Reanimati-on (KPR) sowie ein arterieller pH 7,45 waren mit einem schlechteren Überleben assoziiert. In der zweiten Studie wurden 70 Patienten*innen isoliert mit Impella 5.0/5.5® behandelt. Das 30-Tage-Überleben betrug 51%. Ein präoperativer Anstieg des arteriellen Laktatwertes (OR 1.217 pro 1 mmol/l; p=0.015) sowie KPR (OR 16.74; p=0.009) wurden als Prädiktoren für die 30-Tage-Mortalität identifiziert. Ein arterielles Laktat von 8 mmol/l wies hierbei eine Spezifität von 0.944 und eine Sensitivität von 0.294 (OR 7.083, CI 1.422–35.28; p=0.017). Auf der Basis dieser Daten wurde ein Algorithmus für die Behandlung des KS mittels temporärer MKU entwickelt und folglich im DHZB im Rahmen einer SOP festgelegt. In meiner dritten Analyse haben wir die perkutan implantierbaren Impella CP und die größeren chirurgischen Impella 5.0/5.5® Systeme verglichen. Das nicht adjustierte 30-Tage-Überleben war signifikant höher in der Impella 5.0/5.5® Kohorte (58% vs. 36%, p=0.021). Nach der Propensity-Score-Adjustierung waren die Kohorten ähnlich (OR 1.23, 95% CI [0.34-4.18], p=0.744). Ein präoperativer Laktatwert über 8 mmol/L sowie präoperative KPR gingen mit einer erhöhten Mortalität einher (OR 10.7, 95% CI [3.45-47.34], p<0.001; OR 13.2, 95% CI [4.28-57.89], p<0.001). Der Algorithmus aus der zweiten Studie wurde auf der Basis neuer Ergebnisse um die Anwendung der perkutan implantierbaren Impellerpumpen erweitert. Schlussfolgerung Insgesamt wurden von mir 203 Patienten*innen mit verschiedenen MKU-Systemen ana-lysiert. Unsere Studien haben gezeigt, dass mikroaxiale Impellerpumpen eine effektive Therapie im KS darstellen. Präoperative KPR sowie Laktatwerte ≥ 8 mmol/L sollten eine erweiterte Therapie bestehend aus einer Kombination von einer Impellerpumpe und v-a ECLS nach sich ziehen. Ein Algorithmus basierend auf diesen Erkenntnissen kann helfen eine optimale temporäre MKU-Therapie auszuwählen

Desenvolvimento de comportamentos para robô humanoide

Mestrado em Engenharia de Computadores e TelemáticaHumanoid robotics is an area of active research. Robots with human body are better suited to execute tasks in environments designed for humans. Moreover, people feel more comfortable interacting with robots that have a human appearance. RoboCup encourages robotic research by promoting robotic competitions. One of these competitions is the Standard Platform League (SPL) in which humanoid robots play soccer. The robot used is the Nao robot, created by Aldebaran Robotics. The di erence between the teams that compete in this league is the software that controls the robots. Another league promoted by RoboCup is the 3D Soccer Simulation League (3DSSL). In this league the soccer game is played in a computer simulation. The robot model used is also the one of the Nao robot. However, there are a few di erences in the dimensions and it has one more Degree of Freedom (DoF) than the real robot. Moreover, the simulator cannot reproduce reality with precision. Both these leagues are relevant for this thesis, since they use the same robot model. The objective of this thesis is to develop behaviors for these leagues, taking advantage of the previous work developed for the 3DSSL. These behaviors include the basic movements needed to play soccer, namely: walking, kicking the ball, and getting up after a fall. This thesis presents the architecture of the agent developed for the SPL, which is similar to the architecture of the FC Portugal team agent from the 3DSSL, hence allowing to port code between both leagues easily. It was also developed an interface that allows to control a leg in a more intuitive way. It calculates the joint angles of the leg, using the following parameters: three angles between the torso and the line connecting hip and ankle; two angles between the foot and the perpendicular of the torso; and the distance between the hip and the ankle. It was also developed an algorithm to calculate the three joint angles of the hip that produce the desired vertical rotation, since the Nao robot does not have a vertical joint in the hip. This thesis presents also the behaviors developed for the SPL, some of them based on the existing behaviors from the 3DSSL. It is presented a behavior that allows to create robot movements by de ning a sequence of poses, an open-loop omnidirectional walking algorithm, and a walk optimized in the simulator adapted to the real robot. Feedback was added to this last walk to make it more robust against external disturbances. Using the behaviors presented in this thesis, the robot achieved a forward velocity of 16 cm/s, a lateral velocity of 6 cm/s, and rotated at 40 deg/s. The work developed in this thesis allows to have an agent to control the Nao robot and execute the basic low level behaviors for competing in the SPL. Moreover, the similarities between the architecture of the agent for the SPL with that of the agent from the 3DSSL allow to use the same high level behaviors in both leagues.A robótica humanoide é uma área em ativo desenvolvimento. Os robôs com forma humana estão melhor adaptados para executarem tarefas em ambientes desenhados para humanos. Além disso, as pessoas sentem-se mais confortáveis quando interagem com robôs que tenham aparência humana. O RoboCup incentiva a investigação na área da robótica através da realização de competições de robótica. Uma destas competições é a Standard Platform League (SPL) na qual robôs humanoides jogam futebol. O robô usado é o robô Nao, criado pela Aldebaran Robotics. A diferença entre as equipas que competem nesta liga está no software que controla os robôs. Outra liga presente no RoboCup é a 3D Soccer Simulation League (3DSSL). Nesta liga o jogo de futebol é jogado numa simulação por computador. O modelo de robô usado é também o do robô Nao. Contudo, existem umas pequenas diferenças nas dimensões e este tem mais um grau de liberdade do que o robô real. O simulador também não consegue reproduzir a realidade com perfeição. Ambas estas ligas são importantes para esta dissertação, pois usam o mesmo modelo de robô. O objectivo desta dissertação é desenvolver comportamentos para estas ligas, aproveitando o trabalho prévio desenvolvido para a 3DSSL. Estes comportamentos incluem os movimentos básicos necessários para jogar futebol, nomeadamente: andar, chutar a bola e levantar-se depois de uma queda. Esta dissertação apresenta a arquitetura do agente desenvolvida para a SPL, que é similar á arquitetura do agente da equipa FC Portugal da 3DSSL, para permitir uma mais fácil partilha de código entre as ligas. Foi também desenvolvida uma interface que permite controlar uma perna de maneira mais intuitiva. Ela calcula os ângulos das juntas da perna, usando os seguintes parâmetros: três ângulos entre o torso e a linha que une anca ao tornozelo; dois ângulos entre o pé e a perpendicular do torso; e a distância entre a anca e o tornozelo. Nesta dissertação foi também desenvolvido um algoritmo para calcular os três ângulos das juntas da anca que produzam a desejada rotação vertical, visto o robô Nao não ter uma junta na anca que rode verticalmente. Esta dissertação também apresenta os comportamentos desenvolvidos para a SPL, alguns dos quais foram baseados nos comportamentos já existentes na 3DSSL. É apresentado um modelo de comportamento que permite criar movimentos para o robô de nindo uma sequência de poses, um algoritmo para um andar open-loop e omnidirecional e um andar otimizado no simulador e adaptado para o robô real. A este último andar foi adicionado um sistema de feedback para o tornar mais robusto. Usando os comportamentos apresentados nesta dissertação, o robô atingiu uma velocidade de 16 cm/s para frente, 6 cm/s para o lado e rodou sobre si pr oprio a 40 graus/s. O trabalho desenvolvido nesta dissertação permite ter um agente que controle o robô Nao e execute os comportamentos básicos de baixo nível para competir na SPL. Além disso, as semelhan cas entre a arquitetura do agente para a SPL com a arquitetura do agente da 3DSSL permite usar os mesmos comportamentos de alto nível em ambas as ligas

DESIGN, SYNTHESIS AND MOLECULAR DOCKING STUDY OF HYBRID QUINOLINE-4-YL-OXADIAZOLES/OXATHIADIAZOLES AS POTENT ANTIFUNGAL AGENTS

Objective: The aim of the present work was to design and synthesize hybrid quinoline-4-yl-oxadiazoles/oxathiadiazole derivatives and evaluate them for in vitro antifungal activity against human disease causing pathogens.Methods: The compounds 5(a-d), 6(a-d) and 7(a-d) were efficiently synthesized in good yields. The synthesized compounds were characterized using 1H NMR, 13C NMR and Mass spectra. The synthesized compounds were screened for in vitro antifungal activity and minimum inhibitory concentration (MIC) values were determined using standard agar method. Molecular docking study was performed against fungal enzyme P450 cytochrome lanosterol 14α-demethylase using VLife MDS 4.3 software.Results: The synthesized compounds had shown good to moderate in vitro antifungal activity. The compound 6a (MIC range = 15-25 µg/ml) from 1,2,3,5-oxathiadiazole-2-oxide series showed most potent activity amongst the synthesized compounds when compared with standard clotrimazole (MIC range = 12.5-25 µg/ml). The molecular docking study of synthesized compounds showed good binding interactions against active site of fungal enzyme P450 cytochrome lanosterol 14α-demethylase.Conclusion: The results of in vitro antifungal activity and molecular docking study revealed that the synthesized compounds have potential antifungal activity and can be further optimized and developed as a lead compound.Â

High-throughput detection of mutations responsible for childhood hearing loss using resequencing microarrays

Background: Despite current knowledge of mutations in 45 genes that can cause nonsyndromic sensorineural hearing loss (SNHL), no unified clinical test has been developed that can comprehensively detect mutations in multiple genes. We therefore designed Affymetrix resequencing microarrays capable of resequencing 13 genes mutated in SNHL (GJB2, GJB6, CDH23, KCNE1, KCNQ1, MYO7A, OTOF, PDS, MYO6, SLC26A5, TMIE, TMPRSS3, USH1C). We present results from hearing loss arrays developed in two different research facilities and highlight some of the approaches we adopted to enhance the applicability of resequencing arrays in a clinical setting. Results: We leveraged sequence and intensity pattern features responsible for diminished coverage and accuracy and developed a novel algorithm, sPROFILER, which resolved >80% of no-calls from GSEQ and allowed 99.6% (range: 99.2-99.8%) of sequence to be called, while maintaining overall accuracy at >99.8% based upon dideoxy sequencing comparison. Conclusions: Together, these findings provide insight into critical issues for disease-centered resequencing protocols suitable for clinical application and support the use of array-based resequencing technology as a valuable molecular diagnostic tool for pediatric SNHL and other genetic diseases with substantial genetic heterogeneity

Novel cinnamic acid/4-aminoquinoline conjugates bearing non-proteinogenic amino acids: Towards the development of potential dual action antimalarials

A series of cinnamic acid/4-aminoquinoline conjugates conceived to link, through a proper retro-enantio dipeptide, a heterocyclic core known to prevent hemozoin formation, to a trans-cinnamic acid motif capable of inhibiting enzyme catalytic Cys residues, were synthesized as potential dual-action antimalarials. The effect of amino acid configuration and the absence of the dipeptide spacer were also assessed. The replacement of the D-amino acids by their natural L counterparts led to a decrease in both anti-plasmodial and falcipain inhibitory activity, suggesting that the former are preferable. Molecules with such spacer were active against blood-stage Plasmodium falciparum, in vitro, and hemozoin formation, implying that the dipeptide has a key role in mediating these two activities. In turn, compounds without spacer were better falcipain-2 inhibitors, likely because these compounds are smaller and have their vinyl bonds in closer vicinity to the catalytic Cys, as suggested by molecular modeling calculations. These novel conjugates constitute promising leads for the development of new antiplasmodials targeted at blood-stage malaria parasites